Algae can synthesize, accumulate and store large amounts of lipids in its cells, which holds immense potential as a renewable source of biodiesel. In this work, we have developed and validated a GC–MS method for quantitation of fatty acids and glycerolipids in forms of fatty acid methyl esters derived from algae biomass. Algae Scenedesmus dimorphus drymass was pulverized by mortar and pestle, then extracted by the modified Folch method and fractionated into free fatty acids and glycerolipids on aminopropyl solid-phase extraction cartridges. Fatty acid methyl esters were produced by an optimized one-step esterification of fatty acids and transesterification of glycerolipids with boron trichloride/methanol. The matrix effect, recoveries and stability of fatty acids and glycerolipids in algal matrix were first evaluated by spiking stable isotopes of pentadecanoic-2,2-d2 acid and glyceryl tri(hexadecanoate-2,2-d2) as surrogate analytes and tridecanoic-2,2-d2 acid as internal standard into algal matrix prior to sample extraction. Later, the method was validated in terms of lower limits of quantitation, linear calibration ranges, intra- and inter-assay precision and accuracy using tridecanoic-2,2-d2 acid as internal standard. The method developed has been applied to the quantitation of fatty acid methyl esters from free fatty acid and glycerolipid fractions of algae Scenedesmus dimorphus.